Production of biomass feedstock for methanation in Europe has focused on silages of maize and cereals. As ecological awareness has increased in the last several years, more attention is being focused on perennial energy crops (PECs). Studies of specific PECs have shown that their cultivation may enhance agrobiodiversity and increase soil organic carbon stocks while simultaneously providing valuable feedstock for methanation. This study was designed to compare soil quality indicators under annual energy crops (AECs), PECs and permanent grassland (PGL) on the landscape level in south-western Germany. At a total 25 study sites, covering a wide range of parent materials, the cropping systems were found adjacent to each other. Stands were commercially managed, and PECs included different species such as the Cup Plant, Tall Wheatgrass, Giant Knotweed, Miscanthus, Virginia Mallow and Reed Canary Grass. Soil sampling was carried out for the upper 20 cm of soil. Several soil quality indicators, including soil organic carbon (Corg), soil microbial biomass (Cmic), and aggregate stability, showed that PECs were intermediate between AEC and PGL systems. At landscape level, mean Corg content for (on average) 6.1-year-old stands of PEC was 22.37 (±7.53) g kg1, compared to 19.23 (±8.08) and 32.08 (±10.11) for AEC and PGL. Cmic contents were higher in PECs (356 ± 241 lgCg1) compared to AECs (291 ± 145) but significantly lower than under PGL (753 ± 417). The aggregate stability increased by almost 65% in PECs compared to AEC but was still 57% lower than in PGL. Indicator differences among cropping systems were more pronounced when inherent differences in the parent material were accounted for in the comparisons. Overall, these results suggest that the cultivation of PECs has positive effects on soil quality indicators. Thus, PECs may offer potential to make the production of biomass feedstock more sustainable.